Biology subjects

Stam, M.

Publications and source records attributed to Stam, M..

8 recordsLinked to original sources

bioRxiv2025

Image-based phenotypic sorting of synthetic cells

Understanding the relationships between genotype and phenotype is key to many areas of biological research and to the development of synthetic cells. We describe an image-based screening and sorting workflow that explores the phenotypes of gene-expressing vesicles within nonclonal populations and selects the desired variants. Using automated confocal microscopy and real-time, neural-network-assisted image analysis, we demonstrate that liposomes can be selected for fluorescence intensity, protein localization, membrane morphology, and dynamic behaviors, and their phenotype can be linked to genetic content. This approach could substantially accelerate the evolution of cellular functions in a minimal synthetic context.

synthetic biology↗

bioRxiv2024

Large-Scale Motor Dynamics Associated with Reaching are Altered in Essential Tremor

Essential Tremor (ET) is a very common neurological disorder characterised by involuntary rhythmic movements attributable to pathological synchronization within corticothalamic circuits. Previous work has focused on tremor in isolation, overlooking broader disturbances to motor control during naturalistic movements such as reaching. We hypothesised that ET disrupts the sequential engagement of large-scale rhythmic brain networks, leading to both tremor and deficits in motor planning and execution. To test this, we performed whole-head neuroimaging during an upper-limb reaching task using high-density electroencephalography in ET patients and healthy controls, alongside optically pumped magnetoencephalography in a smaller cohort. Key motor regions--including the supplementary motor area, premotor cortex, posterior parietal cortex, and motor cerebellum--were synchronized to tremor rhythms. Patients exhibited a 15% increase in low beta (14-21 Hz) desynchronization over the supplementary motor area during movement, which strongly correlating with tremor severity (R2 = 0.85). A novel dimensionality reduction technique revealed four distinct networks accounting for 97% of the variance in motor-related brain-wide oscillations, with ET altering their sequential engagement. Consistent with our hypothesis, the frontoparietal beta network- normally involved in motor planning-exhibited additional desynchronization during movement execution in ET patients. This altered engagement correlated with slower movement velocities, suggesting an adaptation towards feedback-driven motor control. These findings reveal fundamental disruptions in distributed motor control networks in ET and identify novel biomarkers as targets for next-generation brain stimulation therapies.

neuroscience↗

bioRxiv2023

RdDM mutants reduce histone methylation rather than DNA methylation at the paramutated maize b1 enhancer

Paramutation is the transfer of mitotically and meiotically heritable silencing information between two alleles. With paramutation at the maize booster1 (b1) locus, the low expressed B epiallele heritably changes the high expressed B-I epiallele into B with 100% frequency. This requires specific tandem repeats and multiple components of the RNA-directed DNA methylation (RdDM) pathway, including the RNA-dependent RNA polymerase (RdRP, mediator of paramutation1, MOP1), the second-largest subunit of RNA polymerase IV and V (NRP(D/E)2a, mediator of paramutation2, MOP2), and the largest subunit of RNA Polymerase IV (NRPD1, mediator of paramutation3, MOP3). Mutations in mop genes prevent paramutation and release silencing at the B epiallele. In this study we investigated the effect of mutations in mop1, mop2 and mop3 on chromatin structure and DNA methylation at the B epiallele, and especially the regulatory hepta-repeat 100 kb upstream of the b1 gene. We show that mutations in mop1 and mop3 result in decreased repressive histone modifications H3K9me2 and H3K27me2 at the hepta-repeat. Associated with this decrease are partial activation of the hepta-repeat enhancer function, formation of a multi-loop structure, and elevated b1 expression. In mop2 mutants, which do not show elevated b1 expression, H3K9me2 and H3K27me2 and a single-loop structure like in wild type B are retained. Surprisingly, high DNA methylation levels at the B hepta-repeat remains in all three mutants. Our results raise the possibility of MOP factors mediating RNA-directed histone methylation rather than RNA-directed DNA methylation at the b1 locus.

plant biology↗

bioRxiv2023

Phenotypic variation in maize can be largely explained by genetic variation at transcription factor binding sites

Comprehensive maps of functional variation at transcription factor (TF) binding sites (cis-elements) are crucial for elucidating how genotype shapes phenotype. Here we report the construction of a pan-cistrome of the maize leaf under well-watered and drought conditions. We quantified haplotype-specific TF footprints across a pan-genome of 25 maize hybrids and mapped over two-hundred thousand genetic variants (termed binding-QTL) linked to cis-element occupancy. Three lines of evidence support the functional significance of binding-QTL: i) they coincide with numerous known causative loci that regulate traits, including VGT1, Trehalase1, and the MITE transposon near ZmNAC111 under drought; ii) their footprint bias is mirrored between inbred parents and by ChIP-seq; iii) partitioning genetic variation across genomic regions demonstrates that binding-QTL capture the majority of heritable trait variation across [~]70% of 143 phenotypes. Our study provides a promising approach to make previously hidden cis-variation more accessible for genetic studies and multi-target engineering of complex traits.

genomics↗

bioRxiv2023

NetSyn: genomic context exploration of protein families

Background: The growing availability of large prokaryotic genomic datasets presents an opportunity to discover new metabolic pathways and enzymatic reactions useful for industrial or synthetic biological applications. Efforts to identify new enzyme functions in this vast number of sequences cannot be achieved without bioinformatics tools and the development of new strategies. Standard methods for assigning a biological function to a gene are based on sequence similarity. However, complementary approaches rely on mine databases to identify conserved gene clusters (i.e. syntenies). In prokaryotic genomes, genes involved in the same pathway are frequently encoded in a single locus with an operonic organisation. This genomic context conservation is considered as a reliable indicator of functional relationships, and is therefore a promising approach for improving the gene function prediction. Methods. Here we present NetSyn (Network Synteny), a tool to group protein sequences based on the conservation of their genomic context rather than solely on sequence similarity. From a list of protein sequence identifiers, NetSyn searches corresponding genome entries to retrieve neighboring genes. Corresponding protein sequences are grouped into families to define homology relationships and compute a synteny conservation score between the different extracted genomic contexts. A network is then created in which the nodes represent the input proteins and the edges indicate that two proteins share a conserved synteny. Finally, the network is partitioned into clusters grouping proteins with similar genomic contexts, using a community detection algorithm. Results. As a proof of concept, we used NetSyn on two different datasets. The first one is the BKACE protein family (formerly named DUF849) which has previously been divided into isofunctional sub-families. NetSyn was able to go a step further by providing additional sub-families beyond those already described. The second dataset corresponds to a set of non-homologous proteins belonging to three different glycoside hydrolase (GH) families. These GHs are known to work cooperatively in a Polysaccharide-Utilization Loci (PUL) and are therefore grouped together in the same genomic contexts. NetSyn was able to identify a locus grouping 3 GHs, involved in the degradation of xyloglucan, in 162 prokaryotic genomes. Discussion. By highlighting conserved synteny in distantly related prokaryotic species, NetSyn enables functional links between proteins to be established beyond sequence similarity alone. We showed that NetSyn is efficient for exploring large prokaryotic protein families, enabling the definition of isofunctional groups and the identification of functional interactions between non-homologous enzymes. These features enable the prediction of new genomic structures that have not yet been experimentally characterized. Finally, NetSyn is also useful for pinpointing annotation errors that have been propagated across databases, and for suggesting annotations on proteins lacking functional prediction. NetSyn is freely available at https://github.com/labgem/netsyn.

bioinformatics↗

bioRxiv2022

Pollen sequencing reveals barriers and aberrant patterns of recombination in interspecific tomato hybrids

Tomato is the most consumed vegetable in the world. Increasing its natural resistance and resilience is key for ensuring food security within a changing climate. Plant breeders improve those traits by generating crosses of cultivated tomatoes with their wild relatives. Specific allele introgression relying on meiotic recombination, is hampered by structural divergence between parental genomes. However, previous studies of interspecific tomato hybridization focused in single cross or lacked resolution due to prohibitive sequencing costs of large segregating populations. Here, we used pooled-pollen sequencing to reveal unprecedented details of recombination patterns in five interspecific tomato hybrids. We detected hybrid-specific recombination coldspots that underscore the influence of structural divergence in shaping recombination landscape. Crossover regions and coldspots show strong association with specific TE superfamilies exhibiting differentially accessible chromatin between somatic and meiotic cells. We also found gene complexes associated with metabolic processes, stress resistance and domestication syndrome traits, revealing undesired consequences of recombination suppression to phenotypes. Finally, we demonstrate that by using resequencing data of wild and domesticated tomato populations, we can screen for alternative parental genomes to overcome recombination barriers. Overall, our results will allow breeders better informed decisions on generating disease-resistant and climate-resilient tomato.

genomics↗

bioRxiv2021

CHROMOMETHYLTRANSFERASE3/KRYPTONITE maintain the sulfurea paramutation in Solanum lycopersicum

Paramutation involves the transfer of a repressive epigenetic mark from a silent allele to an active homologue and, consequently, non-Mendelian inheritance. In tomato the sulfurea (sulf) paramutation is associated with a high level of CHG hypermethylation in a region overlapping the transcription start site of the SlTAB2 gene that affects chlorophyll synthesis. The CCG sub-context hypermethylation is under-represented at this region relative to CTG or CAG implicating the CHROMOMETHYLTRANSFERASE3 (CMT3) in paramutation at this locus. Consistent with this interpretation, loss of CMT3 function leads to loss of the sulf chlorosis, the associated CHG hypermethylation and paramutation. Loss of KRYPTONITE (KYP) histone methyl transferase function has a similar effect linked to reduced H3K9me2 at the promoter region of SlTAB2 and a shift in higher order chromatin structure at this locus. Mutation of the largest subunit of RNA polymerase V (PolV) in contrast does not affect sulf paramutation. These findings indicate the involvement of a CMT3/KYP dependent feedback rather than the PolV-dependent pathway leading to RNA directed DNA methylation (RdDM) in the maintenance of paramutation.

plant biology↗

bioRxiv2020

Identification of key tissue-specific, biological processes by integrating enhancer information in maize gene regulatory networks

Enhancers are important regulators of gene expression during numerous crucial processes including tissue differentiation across development. In plants, their recent molecular characterization revealed their capacity to activate the expression of several target genes through the binding of transcription factors. Nevertheless, identifying these target genes at a genome-wide level remains a challenge, in particular in species with large genomes, where enhancers and target genes can be hundreds of kilobases away. Therefore, the contribution of enhancers to regulatory network is still poorly understood in plants. In this study, we investigate the enhancer-driven regulatory network of two maize tissues at different stages: leaves at seedling stage and husks (bracts) at flowering. Using a systems biology approach, we integrate genomic, epigenomic and transcriptomic data to model the regulatory relationship between transcription factors and their potential target genes. We identify regulatory modules specific to husk and V2-IST, and show that they are involved in distinct functions related to the biology of each tissue. We evidence enhancers exhibiting binding sites for two distinct transcription factor families (DOF and AP2/ERF) that drive the tissue-specificity of gene expression in seedling immature leaf and husk. Analysis of the corresponding enhancer sequences reveals that two different transposable element families (TIR transposon Mutator and MITE Pif/Harbinger) have shaped the regulatory network in each tissue, and that MITEs have provided new transcription factor binding sites that are involved in husk tissue-specificity.Significance Enhancers play a major role in regulating tissue-specific gene expression in higher eukaryotes, including angiosperms. While molecular characterization of enhancers has improved over the past years, identifying their target genes at the genome-wide scale remains challenging. Here, we integrate genomic, epigenomic and transcriptomic data to decipher the tissue-specific gene regulatory network controlled by enhancers at two different stages of maize leaf development. Using a systems biology approach, we identify transcription factor families regulating gene tissue-specific expression in husk and seedling leaves, and characterize the enhancers likely to be involved. We show that a large part of maize enhancers is derived from transposable elements, which can provide novel transcription factor binding sites crucial to the regulation of tissue-specific biological functions.Competing Interest StatementThe authors have declared no competing interest.View Full Text

systems biology↗